2BWD - JenaLib

Title :   ATOMIC RESOLUTION STRUCTURE OF ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE WITH ENDOGENOUSLY BOUND NITRITE AND NO

Authors :   S. V. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain

Date :   13 Jul 05 (Deposition) - 17 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Oxidoreductase, Denitrification, Catalysis, Enzyme Mechanism, Nitrate Assimilation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. V. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
Atomic Resolution Structures Of Resting-State, Substrate- And Product-Complexed Cu-Nitrite Reductase Provide Insight Into Catalytic Mechanism
Proc. Natl. Acad. Sci. Usa V. 102 12041 2005
PubMed-ID: 16093314 | Reference-DOI: 10.1073/PNAS.0504207102

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:95 , CYS A:136 , HIS A:145 , MET A:150	BINDING SITE FOR RESIDUE CU A 501
2	AC2	SOFTWARE	HIS A:100 , HIS A:135 , HIS A:306 , HOA A:506 , NO2 A:507	BINDING SITE FOR RESIDUE CU A 502
3	AC3	SOFTWARE	THR A:228 , GLY A:229 , HIS A:319 , LYS A:321 , HOH A:2340 , HOH A:2556	BINDING SITE FOR RESIDUE ACT A 504
4	AC4	SOFTWARE	GLY A:225 , THR A:228 , PHE A:312 , HIS A:319 , HOH A:2144 , HOH A:2557 , HOH A:2558 , HOH A:2559 , HOH A:2560 , HOH A:2561 , HOH A:2562	BINDING SITE FOR RESIDUE ACT A 505
5	AC5	SOFTWARE	ASP A:98 , HIS A:100 , HIS A:135 , HIS A:255 , ILE A:257 , HIS A:306 , CU A:502 , HOA A:506 , HOH A:2235 , HOH A:2238 , HOH A:2563	BINDING SITE FOR RESIDUE NO2 A 507
6	AC6	SOFTWARE	TRP A:265 , THR A:267 , GLY A:268 , LYS A:269 , ASN A:272 , ASP A:275 , GLN A:278 , HOH A:2466 , HOH A:2564	BINDING SITE FOR RESIDUE ACT A 508
7	AC7	SOFTWARE	ARG A:250 , ASP A:251 , ARG A:253 , ASN A:307 , GLU A:310 , HOH A:2448 , HOH A:2554	BINDING SITE FOR RESIDUE MLI A 503
8	AC8	SOFTWARE	ASP A:98 , HIS A:100 , HIS A:135 , ILE A:257 , HIS A:306 , CU A:502 , NO2 A:507 , HOH A:2238 , HOH A:2563	BINDING SITE FOR RESIDUE HOA A 506

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:334
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:334
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374    
            NIR_ACHCY    45 VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 378
               SCOP domains d2bwda1 A:7-166 Nitrite reductase, NIR                                                                                                                          d2bwda2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains 2bwdA01 A:7-158 Cupredoxins -  blue copper proteins                                                                                                     2bwdA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bwd A   7 VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 340
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (NIR_ACHCY | P25006)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0050421	nitrite reductase (NO-forming) activity	Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0019333	denitrification pathway	The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
	GO:0042128	nitrate assimilation	The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1kcb	CRYSTAL STRUCTURE OF A NO-FORMING NITRITE REDUCTASE MUTANT:AN ANALOG OF A TRANSITION STATE IN ENZYMATIC REACTION
1nia	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : A, B, C; EC: 1.7.99.3; OTHER_DETAILS : PH 6.2 ("62")
1nib	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : A, B, C; EC: 1.7.99.3; OTHER_DETAILS : PH 6.8 ("68")
1nic	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 6.0 ("KP")
1nid	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("NT1") NITRITE SOAKED
1nie	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.0 ("PH5")
1nif	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("T2D") TYPE II COPPER DEPLETED
1rzp	CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH6.2
1rzq	CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH5.0
2nrd	MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("HR")

Description